Summary: Scientists have discovered that all complex systems, whether they are found in the body, in international finance, or in social situations, actually fall into just three basic categories, in terms of how they can be controlled.

We don’t often think of them in these terms, but our brains, global financial markets and groups of friends are all examples of different kinds of complex networks or systems. And unlike the kind of system that exists in your car that has been intentionally engineered for humans to use, these systems are convoluted and not obvious how to control. Economic collapse, disease, and miserable dinner parties may result from a breakdown in such systems, which is why researchers have recently being putting so much energy into trying to discover how best to control these large and important systems.

But now two brothers, Profs. Justin and Derek Ruths, from Singapore University of Technology and Design and McGill University respectively, have suggested, in an article published in Science, that all complex systems, whether they are found in the body, in international finance, or in social situations, actually fall into just three basic categories, in terms of how they can be controlled.

They reached this conclusion by surveying the inputs and outputs and the critical control points in a wide range of systems that appear to function in completely different ways. (The critical control points are the parts of a system that you have to control in order to make it do whatever you want — not dissimilar to the strings you use to control a puppet).

“When controlling a cell in the body, for example, these control points might correspond to proteins that we can regulate using specific drugs,” said Justin Ruths. “But in the case of a national or international economic system, the critical control points could be certain companies whose financial activity needs to be directly regulated.”

One grouping, for example, put organizational hierarchies, gene regulation, and human purchasing behaviour together, in part because in each, it is hard to control individual parts of the system in isolation. Another grouping includes social networks such as groups of friends (whether virtual or real), and neural networks (in the brain), where the systems allow for relatively independent behaviour. The final group includes things like food systems, electrical circuits and the internet, all of which function basically as closed systems where resources circulate internally.

Referring to these groupings, Derek Ruths commented, “While our framework does provide insights into the nature of control in these systems, we’re also intrigued by what these groupings tell us about how very different parts of the world share deep and fundamental attributes in common — which may help unify our understanding of complexity and of control.”

“What we really want people to take away from the research at this point is that we can control these complex and important systems in the same way that we can control a car,” says Justin Ruths. “And that our work is giving us insight into which parts of the system we need to control and why. Ultimately, at this point we have developed some new theory that helps to advance the field in important ways, but it may still be another five to ten years before we see how this will play out in concrete terms.”

Summary: Along with eggs, soup and rubber toys, the list of the chicken’s most lasting legacies may eventually include advanced materials, according to scientists. The researchers report that the unusual arrangement of cells in a chicken’s eye constitutes the first known biological occurrence of a potentially new state of matter known as ‘disordered hyperuniformity,’ which has been shown to have unique physical properties.

Researchers from Princeton University and Washington University in St. Louis report that the unusual arrangement of cells in a chicken’s eye … Credit: Courtesy of Joseph Corbo and Timothy Lau, Washington University in St. Louis

Along with eggs, soup and rubber toys, the list of the chicken’s most lasting legacies may eventually include advanced materials such as self-organizing colloids, or optics that can transmit light with the efficiency of a crystal and the flexibility of a liquid.

The unusual arrangement of cells in a chicken’s eye constitutes the first known biological occurrence of a potentially new state of matter known as “disordered hyperuniformity,” according to researchers from Princeton University and Washington University in St. Louis. Research in the past decade has shown that disordered hyperuniform materials have unique properties when it comes to transmitting and controlling light waves, the researchers report in the journal Physical Review E.

States of disordered hyperuniformity behave like crystal and liquid states of matter, exhibiting order over large distances and disorder over small distances. Like crystals, these states greatly suppress variations in the density of particles — as in the individual granules of a substance — across large spatial distances so that the arrangement is highly uniform. At the same time, disordered hyperuniform systems are similar to liquids in that they have the same physical properties in all directions. Combined, these characteristics mean that hyperuniform optical circuits, light detectors and other materials could be controlled to be sensitive or impervious to certain light wavelengths, the researchers report.

“We’ve since discovered that such physical systems are endowed with exotic physical properties and therefore have novel capabilities,” Torquato said. “The more we learn about these special disordered systems, the more we find that they really should be considered a new distinguishable state of matter.”

The researchers studied the light-sensitive cells known as cones that are in the eyes of chickens and most other birds active in daytime. These birds have four types of cones for color — violet, blue, green and red — and one type for detecting light levels, and each cone type is a different size. The cones are packed into a single epithelial, or tissue, layer called the retina. Yet, they are not arranged in the usual way, the researchers report.

In many creatures’ eyes, visual cells are evenly distributed in an obvious pattern such as the familiar hexagonal compact eyes of insects. In many creatures, the different types of cones are laid out so that they are not near cones of the same type. At first glance, however, the chicken eye appears to have a scattershot of cones distributed in no particular order.

The lab of co-corresponding author Joseph Corbo, an associate professor of pathology and immunology, and genetics at Washington University in St. Louis, studies how the chicken’s unusual visual layout evolved. Thinking that perhaps it had something to do with how the cones are packed into such a small space, Corbo approached Torquato, whose group studies the geometry and dynamics of densely packed objects such as particles.

Torquato then worked with the paper’s first author Yang Jiao, who received his Ph.D. in mechanical and aerospace engineering from Princeton in 2010 and is now an assistant professor of materials science and engineering at Arizona State University. Torquato and Jiao developed a computer-simulation model that went beyond standard packing algorithms to mimic the final arrangement of chicken cones and allowed them to see the underlying method to the madness.

It turned out that each type of cone has an area around it called an “exclusion region” that other cones cannot enter. Cones of the same type shut out each other more than they do unlike cones, and this variant exclusion causes distinctive cone patterns. Each type of cone’s pattern overlays the pattern of another cone so that the formations are intertwined in an organized but disordered way — a kind of uniform disarray. So, while it appeared that the cones were irregularly placed, their distribution was actually uniform over large distances. That’s disordered hyperuniformity, Torquato said.

“Because the cones are of different sizes it’s not easy for the system to go into a crystal or ordered state,” Torquato said. “The system is frustrated from finding what might be the optimal solution, which would be the typical ordered arrangement. While the pattern must be disordered, it must also be as uniform as possible. Thus, disordered hyperuniformity is an excellent solution.”

The researchers’ findings add a new dimension called multi-hyperuniformity. This means that the elements that make up the arrangement are themselves hyperuniform. While individual cones of the same type appear to be unconnected, they are actually subtly linked by exclusion regions, which they use to self-organize into patterns. Multi-hyperuniformity is crucial for the avian system to evenly sample incoming light, Torquato said. He and his co-authors speculate that this behavior could provide a basis for developing materials that can self-assemble into a disordered hyperuniform state.

“You also can think of each one of these five different visual cones as hyperuniform,” Torquato said. “If I gave you the avian system with these cones and removed the red, it’s still hyperuniform. Now, let’s remove the blue — what remains is still hyperuniform. That’s never been seen in any system, physical or biological. If you had asked me to recreate this arrangement before I saw this data I might have initially said that it would be very difficult to do.”

The discovery of hyperuniformity in a biological system could mean that the state is more common than previously thought, said Remi Dreyfus, a researcher at the Pennsylvania-based Complex Assemblies of Soft Matter lab (COMPASS) co-run by the University of Pennsylvania, the French National Centre for Scientific Research and the French chemical company Solvay. Previously, disordered hyperuniformity had only been observed in specialized physical systems such as liquid helium, simple plasmas and densely packed granules.

“It really looks like this idea of hyperuniformity, which started from a theoretical basis, is extremely general and that we can find them in many places,” said Dreyfus, who is familiar with the research but had no role in it. “I think more and more people will look back at their data and figure out whether there is hyperuniformity or not. They will find this kind of hyperuniformity is more common in many physical and biological systems.”

The findings also provide researchers with a detailed natural model that could be useful in efforts to construct hyperuniform systems and technologies, Dreyfus said. “Nature has found a way to make multi-hyperuniformity,” he said. “Now you can take the cue from what nature has found to create a multi-hyperuniform pattern if you intend to.”

Evolutionarily speaking, the researchers’ results show that nature found a unique workaround to the problem of cramming all those cones into the compact avian eye, Corbo said. The ordered pattern of cells in most other animals’ eyes are thought to be the “optimal” arrangement, and anything less would result in impaired vision. Yet, birds with the arrangement studied here — including chickens — have impeccable vision, Corbo said.

“These findings are significant because they suggest that the arrangement of photoreceptors in the bird, although not perfectly regular, are, in fact, as regular as they can be given the packing constraints in the epithelium,” Corbo said.

“This result indicates that evolution has driven the system to the ‘optimal’ arrangement possible, given these constraints,” he said. “We still know nothing about the cellular and molecular mechanisms that underlie this beautiful and highly organized arrangement in birds. So, future research directions will include efforts to decipher how these patterns develop in the embryo.”

The paper, “Avian photoreceptor patterns represent a disordered hyperuniform solution to a multiscale packing problem,” was published Feb. 24 in Physical Review E. The work was supported by grants from the National Science Foundation (grant no. DMS-1211087), National Cancer Institute (grant no. U54CA143803); the National Institutes of Health (grant nos. EY018826, HG006346 and HG006790); the Human Frontier Science Program; the German Research Foundation (DFG); and the Simons Foundation (grant no. 231015).

I began writing this before disaster struck very close to home; and so I finish it without finishing it. A disaster never really ends; it strikes and strikes continuously — and so even silence is insufficient. But yet there is also no expression of concern, no response which could address comprehensively the immense and widespread suffering of bodies and minds and spirits. I would want to emphasize my plea below upon the responsibility of thinkers and artists and writers to create new ways of thinking the disaster; if only to mitigate the possibility of their recurrence. (Is it not the case that the disaster increasingly has the characteristics of the accident; that the Earth and global techno-science are increasingly co-extensive Powers?) And yet despite these necessary new ways of thinking and feeling, I fear it will remain the case that nothing can be said about a disaster, if only because nothing can ultimately be thought about the disaster. But it cannot be simply passed over in silence; if nothing can be said, then perhaps everything may be said.

Inherent to the notion of risk is the multiple, or multiplicity. The distance between the many and the multiple is nearly infinite; every problem of the one and the many resolves to the perspective of the one, while multiplicity always singularizes, takes a line of pure variation or difference to its highest power. A multiplicity is already a life, the sea, time: a cosmos or style in terms of powers and forces; a melody or refrain in its fractured infinity.

The multiple is clear in its “being” only transitorily — as the survey of a fleet or swarm or network; the thought which grasps it climbs mountains, ascends vertiginously towards that infinite height which would finally reveal the substrate of the plane, the “truth” of its shadowy depths, the mysterious origins of its nomadic populations.

No telescopic lens could be large enough to approach this distance; and yet it is traversed instantaneously when the tragic arc of a becoming terminates in disaster; when a line of flight turns into a line of death, when one-or-several lines of organization and development reach a point beyond which avoiding self-destruction is impossible.

Chaos, boundless furnace of becoming! Fulminating entropy which compels even the cosmos itself upon a tragic arc of time; are birth and death not one in chaos or superfusion?

Schizophrenia is perhaps this harrowing recognition that there are only machines machining machines, without limit, bottomless.

In chaos, there is no longer disaster; but there are no longer subjects or situations or signifiers. Every subject, signifier and situation approaches its inevitable as the Disaster which would rend their very being from them; hence the nihilism of the sign, the emptiness of the subject, the void of the situation. Existence is farce — if loss is (permitted to become) tragedy, omnipresent, cosmic, deified.

There is an infinite tragedy at the heart of the disaster; a trauma which makes the truth of our fate impossible-to-utter; on the one hand because imbued with infinite meaning, because singular — and on the other, in turn, meaningless, because essentially nullified, without-reason. That the disaster is never simply pure incidental chaos, a purely an-historical interruption, is perhaps the key point: we start and end with a disaster that prevents us from establishing either end or beginning — a disaster which swiftly looms to cosmic and even ontological proportions…

Perhaps there is only a life after the crisis, after a breakthrough or breakdown; after an encounter with the outside. A life as strategy or risk, which is perhaps to say a multiplicity: a life, or the breakthrough of — and, perhaps inevitably, breakdown before — white walls, mediation, determinacy.

A life in any case is always-already a voice, a cosmos, a thought: it is light or free movement whose origin and destination cannot be identified as stable sites or moments, whose comings and goings are curiously intertwined and undetermined.

We cannot know the limits of a life’s power; but we know disaster. We know that multiplicities, surging flocks of actions and passions, are continually at risk.

The world presents itself unto a life as an inescapable gravity, monstrous fate, the contagion of space, time, organization. A life expresses itself as an openness which is lacerated by the Open.

A life is a cosmos within a cosmos — and so a life opens up closed systems; it struggles and learns not in spite of entropy but on account of it, through a kind of critical strategy, even a perversely recursive or fractal strategy; through the micro-cosmogenetic sieve of organic life, entropy perversely becomes a hyper-organizational principle.

A life enters into a perpetual and weightless ballet — in a defiance-which-is-not-a-defiance of stasis; a stasis which yet presents a grave and continuous danger to a life.

What is a life, apart from infinite movement or disaster? Time, a dream, the sea: but a life moves beyond rivers of time, or seas of dreaming, or the outer spaces of radical forgetting (and alien memories…)

A life is a silence which may become wise. A life — or that perverse machine which works only by breaking down — or through…

A life is intimacy through parasitism, already a desiring-machine-factory or a tensor-calculus of the unconscious.

A life lives in taut suspension from one or several lines of becoming, of flight or death — lines whose ultimate trajectories may not be known through any safe or even sure method.

A life is the torsion between dying and rebirth.

Superfusion between all potentialities, a life is infinite-becoming of the subjectless-subject. Superject.

Journeying and returning, without moving, from the infinity and chaos of the outside/inside. A stationary voyage in a non-dimensional cosmos, where everything flows, heats, grinds.

Phenomenology is a geology of the unconscious, a problem of the crystalline apparatus of time. Could there be at long last a technology of time which would abandon strip-mining the subsconscious?

A communications-strategy, but one that could point beyond the vicious binary of coercion and conflation — but so therefore would not-communicate.

There is a a recursive problem surrounding the silence and darkness at the heart of a life; it is perhaps impossible to exhaust (at least clinically) the infinitely-deferred origin of those crystalline temporal dynamisms which in turn structure any-moment-whatsoever.

Is there a silence which would constitute that very singular machinic ‘sheaf’, the venerated crystalline paradise of the moved-unmoving?

Silence, wisdom.

The impossibility of this origin is also the interminability of the analysis; also the infinite movement attending any moment whatsoever. It is the history of disaster, of the devil.

There is only thinking when a thought becomes critically or clinically engaged with a world, a cosmos. This engagement discovers its bottomlessness in a disaster for thought itself. A disaster for life, thought, the world; but also perhaps their infinitely-deferred origins…

What happens in the physical, economic, social and psychic collapse of a world, a thought, a life? Is it only in this collapse, commensurate with the collision, interference of one cosmos with another…?

Collapse is never a final state. There is no closed system of causes but a kind of original fracture. The schizophrenic coexistence of many separate worlds in a kind of meta-stable superfusion.

A thought, a cosmos, a world, a life can have no other origin than the radical corruption and novel genesis of a pure substance of thinking, living, “worlding,” “cosmosing.” A becoming refracts within its own infinite history the history of a life, a world, a thought.

Although things doubtless seem discouraging, at any moment whatsoever a philosophy can be made possible. At any time and place, this cyclonic involution of the library of Babel can be reactivated, this golden ball propelled by comet-fire and dancing towards the future can be captured in a moment’s reflection…

The breakdown of the world, of thought, of life — the experience of absolute collapse, of the horror of the vacuum, is already close the infinite zero-point reached immediately and effortlessly by schizophrenia. Even in a joyous mode when it recognizes the properly affirmative component of the revelation of cosmos as production, production as multiplicity, multiplicity as it opens onto the infinite or the future. (Only the infinity of the future can become-equal to a life.)

That spirit which fixes a beginning in space and time, fixes it without fixing itself; it exemplifies the possibility of atemporality and the heresy of the asignifying, even while founding the possibility of piety and dogma.

The disaster presents thought and language with their cosmic doubles; thought encounters a disaster in the way a subject encounters a radical outside, a death.

Only selection answers to chaos, to the infinite horizon of a life — virtually mapping infinite potential planes of organization onto a singular line of development. Only selection, only the possibility of philosophy, points beyond the inevitability of disaster.

The disaster and its aversion is the basic orientation of critical thought; thinking the disaster: this impossible task is the critical cultural aim of art and writing. Speaking the truth of the disaster is perhaps impossible. A life encounters disaster as the annihilating of the code itself; not merely a decoding but the alienation from the essence of matter or speech or language. The means to thinking the disaster lie in poetic imagination, the possibility of the temporal retrojection of narrative elements; the disaster can be thought only through “unthinking” it: in the capacity of critical or poetic imagination to explore the means by which a disaster was retroactively averted. The counterfactual acquires a new and radical dimension: not the theological dimension of salvation, but a clinical dimension — the power to of think the transformation of the conditions of the disaster.

ScienceDaily (Aug. 10, 2012) — From protozoans to mammals, evolution has created more and more complex structures and better-adapted organisms. This is all the more astonishing as most genetic mutations are deleterious. Especially in small asexual populations that do not recombine their genes, unfavourable mutations can accumulate. This process is known as Muller’s ratchet in evolutionary biology. The ratchet, proposed by the American geneticist Hermann Joseph Muller, predicts that the genome deteriorates irreversibly, leaving populations on a one-way street to extinction.

In collaboration with colleagues from the US, Richard Neher from the Max Planck Institute for Developmental Biology has shown mathematically how Muller’s ratchet operates and he has investigated why populations are not inevitably doomed to extinction despite the continuous influx of deleterious mutations.

The great majority of mutations are deleterious. “Due to selection individuals with more favourable genes reproduce more successfully and deleterious mutations disappear again,” explains the population geneticist Richard Neher, leader of an independent Max Planck research group at the Max Planck Institute for Developmental Biology in Tübingen, Germany. However, in small populations such as an asexually reproducing virus early during infection, the situation is not so clear-cut. “It can then happen by chance, by stochastic processes alone, that deleterious mutations in the viruses accumulate and the mutation-free group of individuals goes extinct,” says Richard Neher. This is known as a click of Muller’s ratchet, which is irreversible — at least in Muller’s model.

Muller published his model on the evolutionary significance of deleterious mutations in 1964. Yet to date a quantitative understanding of the ratchet’s processes was lacking. Richard Neher and Boris Shraiman from the University of California in Santa Barbara have now published a new theoretical study on Muller’s ratchet. They chose a comparably simple model with only deleterious mutations all having the same effect on fitness. The scientists assumed selection against those mutations and analysed how fluctuations in the group of the fittest individuals affected the less fit ones and the whole population. Richard Neher and Boris Shraiman discovered that the key to the understanding of Muller’s ratchet lies in a slow response: If the number of the fittest individuals is reduced, the mean fitness decreases only after a delay. “This delayed feedback accelerates Muller’s ratchet,” Richard Neher comments on the results. It clicks more and more frequently.

“Our results are valid for a broad range of conditions and parameter values — for a population of viruses as well as a population of tigers.” However, he does not expect to find the model’s conditions one-to-one in nature. “Models are made to understand the essential aspects, to identify the critical processes,” he explains.

In a second study Richard Neher, Boris Shraiman and several other US-scientists from the University of California in Santa Barbara and Harvard University in Cambridge investigated how a small asexual population could escape Muller’s ratchet. “Such a population can only stay in a steady state for a long time when beneficial mutations continually compensate for the negative ones that accumulate via Muller’s ratchet,” says Richard Neher. For their model the scientists assumed a steady environment and suggest that there can be a mutation-selection balance in every population. They have calculated the rate of favourable mutations required to maintain the balance. The result was surprising: Even under unfavourable conditions, a comparably small proportion in the range of several percent of positive mutations is sufficient to sustain a population.

These findings could explain the long-term maintenance of mitochondria, the so-called power plants of the cell that have their own genome and divide asexually. By and large, evolution is driven by random events or as Richard Neher says: “Evolutionary dynamics are very stochastic.”

ScienceDaily (Aug. 10, 2012) — Why, after millions of years of evolution, do organisms build structures that seemingly serve no purpose?

A study conducted at Michigan State University and published in the current issue of The American Naturalist investigates the evolutionary reasons why organisms go through developmental stages that appear unnecessary.

“Many animals build tissues and structures they don’t appear to use, and then they disappear,” said Jeff Clune, lead author and former doctoral student at MSU’s BEACON Center of Evolution in Action. “It’s comparable to building a roller coaster, razing it and building a skyscraper on the same ground. Why not just skip ahead to building the skyscraper?”

Why humans and other organisms retain seemingly unnecessary stages in their development has been debated between biologists since 1866. This study explains that organisms jump through these extra hoops to avoid disrupting a developmental process that works. Clune’s team called this concept the “developmental disruption force.” But Clune says it also could be described as “if the shoe fits, don’t change a thing.”

“In a developing embryo, each new structure is built in a delicate environment that consists of everything that has already developed,” said Clune, who is now a postdoctoral fellow at Cornell University. “Mutations that alter that environment, such as by eliminating a structure, can thus disrupt later stages of development. Even if a structure is not actually used, it may set the stage for other functional tissues to grow properly.”

Going back to the roller coaster metaphor, even though the roller coaster gets torn down, the organism needs the parts from that teardown to build the skyscraper, he added.

“An engineer would simply skip the roller coaster step, but evolution is more of a tinkerer and less of an engineer,” Clune said. “It uses whatever parts that are lying around, even if the process that generates those parts is inefficient.”

An interesting consequence is that newly evolved traits tend to get added at the end of development, because there is less risk of disrupting anything important. That, in turn, means that there is a similarity between the order things evolve and the order they develop.

A new technology called computational evolution allowed the team to conduct experiments that would be impossible to reproduce in nature.

Rather than observe embryos grow, the team of computer scientists and biologists used BEACON’s Avida software to perform experiments with evolution inside a computer. The Avidians — self-replicating computer programs — mutate, compete for resources and evolve, mimicking natural selection in real-life organisms. Using this software, Clune’s team observed as Avidians evolved to perform logic tasks. They recorded the order that those tasks evolved in a variety of lineages, and then looked at the order those tasks developed in the final, evolved organism.

They were able to help settle an age-old debate that developmental order does resemble evolutionary order, at least in this computationally evolving system. Because in a computer thousands of generations can happen overnight, the team was able to repeat this experiment many times to document that this similarity repeatedly occurs.

Additional MSU researchers contributing to the study included BEACON colleagues Richard Lenski, Robert Pennock and Charles Ofria. The research was funded by the National Science Foundation.

ScienceDaily (Aug. 16, 2012) — In uncertain environments, organisms not only react to signals, but also use molecular processes to make guesses about the future, according to a study by Markus Arnoldini et al. from ETH Zurich and Eawag, the Swiss Federal Institute of Aquatic Science and Technology. The authors report in PLoS Computational Biology that if environmental signals are unreliable, organisms are expected to evolve the ability to take random decisions about adapting to cope with adverse situations.

Most organisms live in ever-changing environments, and are at times exposed to adverse conditions that are not preceded by any signal. Examples for such conditions include exposure to chemicals or UV light, sudden weather changes or infections by pathogens. Organisms can adapt to withstand the harmful effects of these stresses. Previous experimental work with microorganisms has reported variability in stress responses between genetically identical individuals. The results of the present study suggest that this variation emerges because individual organisms take random decisions, and such variation is beneficial because it helps organisms to reduce the metabolic costs of protection without compromising the overall benefits.

The theoretical results of this study can help to understand why genetically identical organisms often express different traits, an observation that is not explained by the conventional notion of nature and nurture. Future experiments will reveal whether the predictions made by the mathematical model are met in natural systems.